- Introduction to metabolomics
- Preprocessing of LC-MS data in Bioconductor
12 July 2018
Image of glycolisis https://en.wikipedia.org/wiki/Glycolysis
xcmsreadMSData (MSnbase package):findChromPeaks function, passing settings along with an algorithm-specific parameter object.## Perform centWave peak detection on the MSnExp object cwp <- CentWaveParam(peakwidth = c(2, 10), snthresh = 5) data <- findChromPeaks(data, param = cwp)
TODO add content: - image describing alignment. - available methods. - what is the result? - Caveats: - assumes analytes elute in the same order. - heavily LC setup-dependent.
TODO add content: - image describing the alignment - available methods - what is the result? (m/z - rt ranges).
TODO add content: - what sources of variation? - Crucial to add QC controls in the experiment. - available methods (RUV, linear models). - MS runs not very expensive, running replicates, QC controls etc usually not a problem.
TODO add content: - What databases available - up and coming: compound db, similar to ensembldb and alike. Problem: unclear license situation.
MSnbase).xcms.